relax SVN archive

Merged revisions 22511,22514-22515,22522-22529,22612,22614-22617,22622-22625 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22511 | bugman | 2014-03-19 10:45:46 +0100 (Wed, 19 Mar 2014) | 6 lines

The AXIS_ALPHA parameter is now initialised in the CaM frame order system test base script.

The base script was broken a while back (r22192) due to AXIS_ALPHA not being defined but being
checked for.
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r22514 | bugman | 2014-03-21 09:17:23 +0100 (Fri, 21 Mar 2014) | 5 lines

Improvements for the centre of mass calculation for the frame order model optimisation.

This is now only calculated for the rotor models. The CoM is also printed out for better user feedback.
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r22515 | bugman | 2014-03-21 09:39:33 +0100 (Fri, 21 Mar 2014) | 7 lines

The CaM frame order system tests for the rotor models are converted to the new axis_alpha parameter.

The axis_theta and axis_phi spherical coordinates are converted to the new reduced parameter set
defined by a random point in space (the CoM of all atoms), the pivot point, and a single angle
alpha.
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r22522 | bugman | 2014-03-24 17:15:10 +0100 (Mon, 24 Mar 2014) | 5 lines

The CaM frame order system test base script is now using lib.geometry.vectors.vector_angle().

This is for correctly calculating the alpha axis angle for the rotor models.
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r22523 | bugman | 2014-03-25 08:51:56 +0100 (Tue, 25 Mar 2014) | 7 lines

Fixes for the rotor axis alpha angle conversion in the CaM frame order system test base script.

The pivot point is not the point on the rotor axis closest to the reference point (the CoM).
Therefore the closest point is now calculated from the pivot point on the axis and the axis vector.
This closest point is needed for defining the new minimal parameter set for the rotor models.
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r22524 | bugman | 2014-03-25 10:00:04 +0100 (Tue, 25 Mar 2014) | 6 lines

Changes for the convert_rotor() method of the CaM frame order system test base script.

The method now sets the alpha angle rather than returning it. The method now also resets the pivot
point to the point on the rotation axis closest to the CoM.
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r22525 | bugman | 2014-03-25 10:08:00 +0100 (Tue, 25 Mar 2014) | 6 lines

Fixes for the rotor axis reconstruction in the func_rotor_qrint() frame order target function.

This is for the rotor model. The axis alpha angle is now correctly converted into the rotor axis
using the CoM and pivot point.
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r22526 | bugman | 2014-03-25 10:26:03 +0100 (Tue, 25 Mar 2014) | 5 lines

Optimisation is now turned on for the Frame_order.test_cam_rotor2 system test.

This is to reveal deficiencies in the handling of the new axis alpha parameter.
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r22527 | bugman | 2014-03-25 10:37:49 +0100 (Tue, 25 Mar 2014) | 5 lines

The frame order optimisation results unpacking function now supports the axis alpha parameter.

This is in the function specific_analyses.frame_order.optimisation.unpack_opt_results().
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r22528 | bugman | 2014-03-25 11:33:22 +0100 (Tue, 25 Mar 2014) | 6 lines

Updated the chi2 value check in some of the CaM frame order system tests for the rotor model.

The chi2 value is slightly different due to truncation and conversion artifacts of the parameter set
reduction.
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r22529 | bugman | 2014-03-25 17:36:10 +0100 (Tue, 25 Mar 2014) | 6 lines

Shifted all of the code for calculating the frame order rotor axis into lib.frame_order.rotor_axis.

The new frame_order.rotor_axis module consists of three function for creating a unit vector or the
rotor axis using either the axis alpha angle, the two spherical angles or the three Euler angles.
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r22612 | bugman | 2014-03-31 08:36:59 +0200 (Mon, 31 Mar 2014) | 3 lines

Import fix.
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r22614 | bugman | 2014-03-31 10:07:25 +0200 (Mon, 31 Mar 2014) | 5 lines

Renamed the specific_analyses.frame_order.user_functions module to uf.

This is to match the changes in trunk.
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r22615 | bugman | 2014-03-31 10:52:12 +0200 (Mon, 31 Mar 2014) | 9 lines

Reverted r22192 as the parameter conversion is now performed by the base script.

This is only for the rotor CaM frame order system test script. The changes to the base script have
already been rewritten.

The command used was:
svn merge -r22192:22191 test_suite/system_tests/scripts/frame_order/cam/rotor.py
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r22616 | bugman | 2014-03-31 15:53:03 +0200 (Mon, 31 Mar 2014) | 5 lines

Fix for the optimised chi-squared value check in the Frame_order.test_cam_rotor system test.

The reduced parameter set results in a slightly different chi2 value.
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r22617 | bugman | 2014-03-31 16:23:19 +0200 (Mon, 31 Mar 2014) | 3 lines

Shifted the frame order average domain position info check from the 'optimisation' to 'checks' module.
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r22622 | bugman | 2014-04-03 13:26:47 +0200 (Thu, 03 Apr 2014) | 7 lines

Fix for the CaM frame order system tests.

The axis alpha angle and pivot shifting to the closest point to the CoM in the base system test
script now only happens for the 'rotor' and 'free rotor' models. This allows the tests for the
isotropic cone models to pass again.
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r22623 | bugman | 2014-04-03 18:24:17 +0200 (Thu, 03 Apr 2014) | 3 lines

Fixed a missing import.
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r22624 | bugman | 2014-04-03 18:30:35 +0200 (Thu, 03 Apr 2014) | 5 lines

Fixes for all of the CaM frame order optimisation scripts in the test data directories.

The frame_order.average_position user function is now essential.
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r22625 | bugman | 2014-04-03 19:13:43 +0200 (Thu, 03 Apr 2014) | 5 lines

The centre of mass printout in the frame order target function setup now uses the verbosity argument.

This means that the printout is not shown for the Monte Carlo simulation optimisation.
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Merged revisions 22176-22178,22192-22194 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22176 | bugman | 2014-02-12 14:56:21 +0100 (Wed, 12 Feb 2014) | 7 lines

Changes to the frame_order.pivot user function.

The 'order' argument has been added to allow for multiple pivots to be present. The user function
backend will store these as cdp.pivot, cdp.pivot2, cdp.pivot3, etc. The 'fix' argument is now
defaulting to False to make sure it is always boolean.
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r22177 | bugman | 2014-02-12 16:20:38 +0100 (Wed, 12 Feb 2014) | 3 lines

The second pivot is now being passed into the frame order target function class.
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r22178 | bugman | 2014-02-13 09:55:09 +0100 (Thu, 13 Feb 2014) | 6 lines

Simplified the CaM frame order system test base script.

The class variables are now always defined, so checking for their existence is pointless. The
CONE_S1 is now also defined in the base script as a class variable.
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r22192 | bugman | 2014-02-14 17:25:00 +0100 (Fri, 14 Feb 2014) | 10 lines

Converted the Frame_order.test_cam_rotor system script test to use the new rotor model parameters.

The rotor frame order parameters {P_alpha, P_beta, P_gamma, T_x, T_y, T_z, E_theta, E_phi, p_x, p_y,
p_z}, where P_i are the Euler angles defining the average domain position, T_i are the translations
defining the average domain position, E_i are the Eigenframe angles defining the rotation axis, and
p_i are the pivot point coordinates, will be converted to {P_alpha, P_beta, P_gamma, T_x, T_y, T_z,
Ax_alpha, p_x, p_y, p_z}. Ax_alpha is the new parameter which defines the rotation axis together
with the pivot using the minimal parameter set {p_x, p_y, p_z, Ax_alpha}.
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r22193 | bugman | 2014-02-14 17:26:33 +0100 (Fri, 14 Feb 2014) | 3 lines

Added support for the new axis_alpha frame order parameter to the specific_analyses.frame_order package.
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r22194 | bugman | 2014-02-14 17:54:31 +0100 (Fri, 14 Feb 2014) | 6 lines

Implemented the new frame order rotor model parameters in the target function.

The parameters {axis_theta, axis_phi} have been replaced by the single axis_alpha. To support the
new model construct, the CoM of the entire system is now passed into the target function.
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Merged revisions 22171-22175 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22171 | bugman | 2014-02-12 09:30:17 +0100 (Wed, 12 Feb 2014) | 3 lines

Capitalised the class variables of all of the CaM frame order system test scripts.
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r22172 | bugman | 2014-02-12 10:14:05 +0100 (Wed, 12 Feb 2014) | 6 lines

Class variable cleanup for the CaM frame order system test scripts.

The variables are now all defined in the base script and only overwritten when needed by the
individual tests.
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r22173 | bugman | 2014-02-12 10:16:47 +0100 (Wed, 12 Feb 2014) | 3 lines

Updated the test_suite.system_tests.scripts.frame_order.cam package __all__ list.
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r22174 | bugman | 2014-02-12 11:14:09 +0100 (Wed, 12 Feb 2014) | 6 lines

Changed the handling of the pivot point in the CaM frame order system tests.

The pivot point is now a class variable, rather than being hardcoded into a function. The handling
of a second pivot has also been added.
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r22175 | bugman | 2014-02-12 11:15:07 +0100 (Wed, 12 Feb 2014) | 3 lines

Updated the CaM frame order double rotor system test script to have the correct two pivots.
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Merged revisions 22170 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22170 | bugman | 2014-02-12 09:13:08 +0100 (Wed, 12 Feb 2014) | 3 lines

Added a simple script for analysing the Eigensystem of the CaM frame order double rotor test model.
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Merged revisions 22169 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22169 | bugman | 2014-02-10 17:48:18 +0100 (Mon, 10 Feb 2014) | 3 lines

Import fix for the changes to the specific_analyses.frame_order package layout.
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Merged revisions 22140-22142 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22140 | bugman | 2014-02-07 08:51:59 +0100 (Fri, 07 Feb 2014) | 6 lines

The double rotor system is now truly perpendicular.

This is for the CaM frame order synthetic test data. The two axes were not perpendicular whereas
for the model they should be.
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r22141 | bugman | 2014-02-07 09:04:11 +0100 (Fri, 07 Feb 2014) | 6 lines

Updated the double rotor distribution PDB file for the perpendicular axes.

This is for the CaM frame order double rotor synthetic data. The number of structures in this
distribution is set to 100 (10 per motional mode). The PyMOL *.pse file has also been updated.
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r22142 | bugman | 2014-02-07 10:44:54 +0100 (Fri, 07 Feb 2014) | 6 lines

Updated the CaM frame order double rotor synthetic test data for the perpendicular axes.

The RDC and PCS data has been recalculated for 250,000 structures, this time with the axes being
truly perpendicular.
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Merged revisions 22114 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22114 | bugman | 2014-02-04 10:24:23 +0100 (Tue, 04 Feb 2014) | 7 lines

Changed the precision of the deactivated Frame_order.test_cam_double_rotor_pcs system test.

This test will run with the command "relax -s Frame_order.test_cam_double_rotor_pcs" and, because of
the small angle of the test model, the chi-squared value differences for just the PCS were too small
for the previous precision of 1 decimal place.
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Merged revisions 22109-22112 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22109 | bugman | 2014-02-03 12:36:46 +0100 (Mon, 03 Feb 2014) | 3 lines

Copyright notice update.
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r22110 | bugman | 2014-02-03 13:35:23 +0100 (Mon, 03 Feb 2014) | 7 lines

Initial implementation of the lib.frame_order.double_rotor module.

This module implements the functions needed to solve the frame order analysis for the RDC (via the
frame order matrix) and PCS (numerically). The interfaces have been updated for the double rotor
but most of the code still implements the basic rotor model from which it derives.
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r22111 | bugman | 2014-02-03 15:14:22 +0100 (Mon, 03 Feb 2014) | 5 lines

Fix for the double rotor frame order model when only RDCs are used.

The target function was not being aliased when no PCS data was present.
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r22112 | bugman | 2014-02-03 15:26:28 +0100 (Mon, 03 Feb 2014) | 3 lines

Removal of unused imports from the lib.frame_order.double_rotor module.
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Merged revisions 22106-22107 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22106 | bugman | 2014-01-31 17:26:59 +0100 (Fri, 31 Jan 2014) | 3 lines

Better support for the parameters of the double rotor frame order model.
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r22107 | bugman | 2014-01-31 17:32:20 +0100 (Fri, 31 Jan 2014) | 7 lines

Initial implementation of the double rotor frame order model target function.

The target function func_double_rotor() has been created as a copy of the func_rotor_qrint() method,
modified for the double rotor model. Modifications will likely be needed as the
compile_2nd_matrix_double_rotor() and pcs_numeric_int_double_rotor() functions are implemented.
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Merged revisions 22073 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/double_rotor

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r22073 | bugman | 2014-01-30 14:36:43 +0100 (Thu, 30 Jan 2014) | 3 lines

Added the double rotor frame order model to the frame_order.select_model user function.
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